|
| Status |
Public on Sep 27, 2013 |
| Title |
H3k4me3 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
H3k4me3 IP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC-3
chip antibody: anti-H3k4me3; Millipore (#07-473)
|
| Treatment protocol |
na
|
| Growth protocol |
PC3 cells grown at exponential phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Eluates from two ChIPs were pooled and prepared as a single library using the standard Illumina ChIP-seq library preparation protocol. Briefly, ~10 ng of input and ChIPed DNA were end-repaired followed by addition of “A” base to the 3’ end of the DNA fragments. The resulting modified DNA fragments were then ligated to the oligonucleotide adaptors and PCR amplified to construct the libraries. The libraries were size-selected in 200-300 bp range by agarose gel purification. Prior to sequencing, sample quality was assessed using Bioanalyzer Hypersensitive DNA kit (Agilent). Library concentration was confirmed by qPCR. Samples were diluted to 10 nM and sent to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley (http://qb3.berkeley.edu/gsl) for sequencing analysis on Illumina Hiseq2000 sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA_v1.8.0. was used for base-calling
alignment to human genome was performed with bowtie (version 0.12.7)
filtering: reads mapped to multiple genomic regions were removed from the analysis
peak-calling was performed with CCAT (version 3.0) using Input DNA as control (*peak.txt files)
Genome_build: Hg19
|
| |
|
| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vera Huang |
| E-mail(s) |
vhuang2013@gmail.com
|
| Organization name |
UCSF
|
| Department |
Urology
|
| Lab |
Long-Cheng Li Lab
|
| Street address |
1450 Third Street, Helen Diller Cancer Research Building, Room 302
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE40536 |
Genome-wide profiling of Argonaute-chromosome interactions [ChIP-Seq] |
|
| Relations |
| SRA |
SRX181769 |
| BioSample |
SAMN01141838 |
